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Old 12-11-2009, 02:09 PM   #1
DrD2009
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Default Novice Problem with Tophat

Brand new to using Tophat so I tried running the test_data from the site to check my installations of Bowtie and Tophat. Tophat starts to work, but then stops.

root@kc-bio-bsb319debian:/home/bldf2b/Desktop/test_data# tophat -r 20 test_ref reads_1.fq reads_2.fq

[Fri Dec 11 16:03:43 2009] Beginning TopHat run (v1.0.11)
-----------------------------------------------
[Fri Dec 11 16:03:43 2009] Preparing output location ./tophat_out/
[Fri Dec 11 16:03:43 2009] Checking for Bowtie index files
[Fri Dec 11 16:03:43 2009] Checking for reference FASTA file
[Fri Dec 11 16:03:43 2009] Checking for Bowtie
Bowtie version: 0.11.3.0
[Fri Dec 11 16:03:43 2009] Checking reads
seed length: 75bp
format: fastq
quality scale: --phred33-quals
root@kc-bio-bsb319debian:/home/bldf2b/Desktop/test_data#


Any ideas? Thanks.
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Old 12-14-2009, 12:54 PM   #2
shurjo
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Can you post here the content from the log files in the tophat_out directory that was created when you ran the job? That would help me to see if the source of the problem can be pinpointed.
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Old 12-14-2009, 01:15 PM   #3
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This is the only line contained within the tophat_out/logs/run.log file

/usr/local/bin/tophat -r 20 test_ref reads_1.fq reads_2.fq
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Old 12-14-2009, 01:23 PM   #4
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It seems that it didn't even pass the read checking stage. Did you see an error message in prep_reads.log?
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Old 12-14-2009, 01:27 PM   #5
DrD2009
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The only file under tophat_out/logs is the run.log file with that one line of text. No prep_reads.log was created.
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Old 12-29-2009, 08:19 AM   #6
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Any more ideas or possible solutions?

The only thing I could think of is maybe Tophat being installed improperly, but since it's running I'm assuming it is installed correctly. I'm kind of dead in the water until I solve this problem and I'm not sure where to go from here.
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Old 12-29-2009, 02:22 PM   #7
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Did the test_data file works?
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Old 12-29-2009, 02:29 PM   #8
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No. That is what I was attempting to run to check everything out. The output from the run is in my first post.

I'm not sure why it simply stops and doesn't continue processing as it shows on the tutorial page (http://tophat.cbcb.umd.edu/tutorial.html).
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Old 12-29-2009, 02:49 PM   #9
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Oh, yes I see.
Don't know if this will help you but did you try to test if you can align the two *.fq files against the test_ref with bowtie along?
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Old 12-30-2009, 11:49 AM   #10
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Both the fastq files map to the test_ref just fine using bowtie and no problems occur.

I came up with my own index and fastq files to try with tophat and the results were exactly the same, it goes to the quality scale line and then just stops processing.
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Old 12-30-2009, 01:24 PM   #11
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Maybe upgrading to tophat 1.0.12 will help.Could be that tophat 1.0.11 doesn't go well with bowtie 0.11.3? Just tried tophat 1.0.11 with bowtie 0.11.3 and the test_data failed, although at a later stage of the run.
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